Give TJ a shout. I'd recommend the Soilfloc, he can help with application. In any case I'd recommend cleaning all the cover out from inside the pond so the bottom is clean before applying it, that way it can get to the whole pond bottom. Then put the cover (habitat) back in the pond. I know, I know, a PITA.
Did the NRCS give you any idea on how many acres of watershed feeds the pond? It just sounds like the pond isn't sealed and any water that gets in there leaks out, but that is an observation from here, not on-site.
You will also need to put down erosion matting to stop erosion. Look for erosion mat that is 100% organic, with jute fibers and not plastic mesh/netting. The plastic mesh/netting, when under water can act as a gill net, catching a lot of fish. It won't decompose like the jute erosion mat. The erosion mat is needed so the soilfloc isn't washed into the pond as it fills, causing a potential leak where the soil is eroded away.
